to update vep: 1) delete variant_effect_predictor dir (leave symlink intact) 2) download latest version from: http://www.ensembl.org/info/docs/tools/vep/index.html 3) run INSTALL.pl - skip libraries 4) rename Bio to eg Bio.v7x and update Bio symlink in ~/perl5/lib/perl5 5) download & extract matching databases into ~/.vep/core & ~/.vep/refseq using ftp://ftp.ensembl.org/pub/release-<xx>/variation/VEP/